SPRTN Gene (Protein Coding)

SprT-Like N-Terminal Domain

GC01P231337
GIFtS:
35
The protein encoded by this gene may play a role in DNA repair during replication of damaged DNA. This protein recruits valosin containing protein (p97) to stalled DNA replication forks where it may prevent excessive translesional DNA synthesis and limit the number of DNA-damage induced mutations. It may also be involved in replication-related G2/M-checkpoint regulation. Defici... See more...

Aliases for SPRTN Gene

Aliases for SPRTN Gene

  • SprT-Like N-Terminal Domain 2 3 5
  • SprT-Like Domain-Containing Protein Spartan 3 4
  • DNA Damage-Targeting VCP (P97) Adaptor 2 3
  • DNA Damage Protein Targeting VCP 3 4
  • C1orf124 3 4
  • Spartan 3 4
  • DVC1 3 4
  • Protein With SprT-Like Domain At The N Terminus 4
  • Zinc Finger RAD18 Domain-Containing Protein 3
  • Chromosome 1 Open Reading Frame 124 2
  • SprT-Like Domain At The N Terminus 2
  • PRO4323 3

External Ids for SPRTN Gene

Previous HGNC Symbols for SPRTN Gene

  • C1orf124

Previous GeneCards Identifiers for SPRTN Gene

  • GC01P231473

Summaries for SPRTN Gene

Entrez Gene Summary for SPRTN Gene

  • The protein encoded by this gene may play a role in DNA repair during replication of damaged DNA. This protein recruits valosin containing protein (p97) to stalled DNA replication forks where it may prevent excessive translesional DNA synthesis and limit the number of DNA-damage induced mutations. It may also be involved in replication-related G2/M-checkpoint regulation. Deficiency of a similar protein in mouse causes chromosomal instability and progeroid phenotypes. Mutations in this gene have been associated with Ruijs-Aalfs syndrome (RJALS). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]

GeneCards Summary for SPRTN Gene

SPRTN (SprT-Like N-Terminal Domain) is a Protein Coding gene. Diseases associated with SPRTN include Ruijs-Aalfs Syndrome. Among its related pathways are DNA Double-Strand Break Repair and Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template. Gene Ontology (GO) annotations related to this gene include ubiquitin binding and K63-linked polyubiquitin modification-dependent protein binding.

UniProtKB/Swiss-Prot Summary for SPRTN Gene

  • Regulator of UV-induced DNA damage response: acts as a 'reader' of ubiquitinated PCNA that enhances RAD18-mediated PCNA ubiquitination and translesion DNA synthesis (TLS). Recruited to sites of UV damage and interacts with ubiquitinated PCNA and RAD18, the E3 ubiquitin ligase that monoubiquitinates PCNA. Facilitates chromatin association of RAD18 and is required for efficient PCNA monoubiquitination, promoting a feed-forward loop to enhance PCNA ubiquitination and translesion DNA synthesis. Acts as a regulator of TLS by recruiting VCP/p97 to sites of DNA damage, possibly leading to extraction of DNA polymerase eta (POLH) by VCP/p97 to prevent excessive translesion DNA synthesis and limit the incidence of mutations induced by DNA damage.

Gene Wiki entry for SPRTN Gene

Additional gene information for SPRTN Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPRTN Gene

Genomics for SPRTN Gene

GeneHancer (GH) Regulatory Elements for SPRTN Gene

Promoters and enhancers for SPRTN Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPRTN on UCSC Golden Path with GeneCards custom track

Genomic Locations for SPRTN Gene

Genomic Locations for SPRTN Gene
chr1:231,337,104-231,370,551
(GRCh38/hg38)
Size:
33,448 bases
Orientation:
Plus strand
chr1:231,472,850-231,490,769
(GRCh37/hg19)
Size:
17,920 bases
Orientation:
Plus strand

Genomic View for SPRTN Gene

Genes around SPRTN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPRTN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPRTN Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SPRTN Gene

Proteins for SPRTN Gene

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  • Protein details for SPRTN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H040-SPRTN_HUMAN
    Recommended name:
    SprT-like domain-containing protein Spartan
    Protein Accession:
    Q9H040
    Secondary Accessions:
    • B1AKT0
    • B5MEF7
    • Q5TE78
    • Q6UWW6
    • Q96BC5
    • Q96KA0

    Protein attributes for SPRTN Gene

    Size:
    489 amino acids
    Molecular mass:
    55134 Da
    Quaternary structure:
    • Interacts with PCNA (when ubiquitinated). Interacts with RAD18. Interacts (via its SHP-box) with VCP/p97. Interacts with KCTD13 and POLD3.
    SequenceCaution:
    • Sequence=BAB55037.1; Type=Frameshift; Positions=224; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SPRTN Gene

    Alternative splice isoforms for SPRTN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPRTN Gene

Post-translational modifications for SPRTN Gene

  • Ubiquitination at Lys84, Lys98, Lys203, Lys271, Lys280, Lys341, Lys361, Lys407, Lys414, Lys423, Lys424, and Lys435
  • Modification sites at PhosphoSitePlus

Other Protein References for SPRTN Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPRTN Gene

Domains & Families for SPRTN Gene

Gene Families for SPRTN Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SPRTN Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPRTN Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger RAD18 domain-containing protein C1orf124 (CA124_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H040

UniProtKB/Swiss-Prot:

SPRTN_HUMAN :
  • The PIP-box mediates the interaction with PCNA, while the UBZ-type zinc finger mediates binding to 'Lys-48'- and 'Lys-63'-linked polyubiquitin (PubMed:22894931, PubMed:22681887, PubMed:23042607, PubMed:23042605 and PubMed:22987070).
  • Belongs to the Spartan family.
Domain:
  • The PIP-box mediates the interaction with PCNA, while the UBZ-type zinc finger mediates binding to 'Lys-48'- and 'Lys-63'-linked polyubiquitin (PubMed:22894931, PubMed:22681887, PubMed:23042607, PubMed:23042605 and PubMed:22987070).
Family:
  • Belongs to the Spartan family.
genes like me logo Genes that share domains with SPRTN: view

Function for SPRTN Gene

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Molecular function for SPRTN Gene

UniProtKB/Swiss-Prot Function:
Regulator of UV-induced DNA damage response: acts as a 'reader' of ubiquitinated PCNA that enhances RAD18-mediated PCNA ubiquitination and translesion DNA synthesis (TLS). Recruited to sites of UV damage and interacts with ubiquitinated PCNA and RAD18, the E3 ubiquitin ligase that monoubiquitinates PCNA. Facilitates chromatin association of RAD18 and is required for efficient PCNA monoubiquitination, promoting a feed-forward loop to enhance PCNA ubiquitination and translesion DNA synthesis. Acts as a regulator of TLS by recruiting VCP/p97 to sites of DNA damage, possibly leading to extraction of DNA polymerase eta (POLH) by VCP/p97 to prevent excessive translesion DNA synthesis and limit the incidence of mutations induced by DNA damage.

Phenotypes From GWAS Catalog for SPRTN Gene

Gene Ontology (GO) - Molecular Function for SPRTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 22681887
GO:0043130 ubiquitin binding IDA 22681887
GO:0046872 metal ion binding IEA --
GO:0070530 K63-linked polyubiquitin modification-dependent protein binding IDA 22681887
genes like me logo Genes that share ontologies with SPRTN: view
genes like me logo Genes that share phenotypes with SPRTN: view

Human Phenotype Ontology for SPRTN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SPRTN Gene

MGI Knock Outs for SPRTN:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPRTN

Clone Products

  • Addgene plasmids for SPRTN

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SPRTN Gene

Localization for SPRTN Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPRTN Gene

Nucleus. Chromosome. Note=Localizes to sites of UV damage via the PIP-box. Recruited to stalled replication forks at sites of replication stress.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPRTN gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPRTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IBA 22681887
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with SPRTN: view

Pathways & Interactions for SPRTN Gene

genes like me logo Genes that share pathways with SPRTN: view

Gene Ontology (GO) - Biological Process for SPRTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006974 cellular response to DNA damage stimulus IDA,IBA 22681887
GO:0009411 response to UV IDA 22681887
GO:0019985 translesion synthesis IMP 23042605
GO:0031398 positive regulation of protein ubiquitination IDA 22681887
genes like me logo Genes that share ontologies with SPRTN: view

No data available for SIGNOR curated interactions for SPRTN Gene

Drugs & Compounds for SPRTN Gene

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  1. Drug
No Compound Related Data Available

Transcripts for SPRTN Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SPRTN Gene

(3) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(108) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPRTN

Clone Products

  • Addgene plasmids for SPRTN

Alternative Splicing Database (ASD) splice patterns (SP) for SPRTN Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b
SP1: -
SP2: - -
SP3:

Relevant External Links for SPRTN Gene

GeneLoc Exon Structure for
SPRTN
ECgene alternative splicing isoforms for
SPRTN

Expression for SPRTN Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPRTN Gene

mRNA expression in normal human tissues for SPRTN Gene
mRNA expression by GTEx for SPRTN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of SPRTN Gene:

SPRTN

SOURCE GeneReport for Unigene cluster for SPRTN Gene:

Hs.554892

Evidence on tissue expression from TISSUES for SPRTN Gene

  • Nervous system(4.3)
  • Intestine(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SPRTN Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • cheek
  • chin
  • eye
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • liver
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SPRTN: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SPRTN Gene

Orthologs for SPRTN Gene

This gene was present in the common ancestor of animals.

Orthologs for SPRTN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SPRTN 33 32
  • 99.52 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia SPRTN 33 32
  • 86.64 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia SPRTN 33 32
  • 82.92 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Sprtn 32
  • 75.67 (n)
mouse
(Mus musculus)
 Mammalia Sprtn 17 33 32
  • 74.5 (n)
oppossum
(Monodelphis domestica)
 Mammalia SPRTN 33
  • 66 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia SPRTN 33
  • 6 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves C3H1ORF124 32
  • 59.24 (n)
SPRTN 33
  • 44 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SPRTN 33
  • 51 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia sprtn 32
  • 57.91 (n)
zebrafish
(Danio rerio)
 Actinopterygii LOC101886162 32
  • 60.62 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG9203 33
  • 22 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea dvc-1 33
  • 44 (a)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 33
  • 52 (a)
 OneToOne
Species where no ortholog for SPRTN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SPRTN Gene

ENSEMBL:
Gene Tree for SPRTN (if available)
TreeFam:
Gene Tree for SPRTN (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPRTN: view image

Paralogs for SPRTN Gene

No data available for Paralogs for SPRTN Gene

Variants for SPRTN Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for SPRTN Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs483352868 uncertain-significance, Joubert syndrome 231,336,952(+) T/C upstream_transcript_variant
rs527236212 pathogenic, Ruijs-Aalfs syndrome 231,352,612(+) AAA/AA 3_prime_UTR_variant, coding_sequence_variant, frameshift
rs527236213 pathogenic, Ruijs-Aalfs syndrome, Ruijs-Aalfs syndrome (RJALS) [MIM:616200] 231,347,825(+) A/G coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, missense_variant, upstream_transcript_variant
rs587593493 pathogenic, Ruijs-Aalfs syndrome, not provided 231,351,570(+) AGGTA/A coding_sequence_variant, frameshift, intron_variant, splice_donor_variant
rs1000012705 -- 231,338,047(+) T/G 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SPRTN Gene

Variant ID Type Subtype PubMed ID
esv3589109 CNV loss 21293372
nsv819245 CNV loss 19587683

Variation tolerance for SPRTN Gene

Residual Variation Intolerance Score: 43.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.89; 35.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPRTN Gene

Human Gene Mutation Database (HGMD)
SPRTN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPRTN

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPRTN Gene

Disorders for SPRTN Gene

MalaCards: The human disease database

(1) MalaCards diseases for SPRTN Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
ruijs-aalfs syndrome
  • rjals
- elite association - COSMIC cancer census association via MalaCards
Search SPRTN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SPRTN_HUMAN
  • Ruijs-Aalfs syndrome (RJALS) [MIM:616200]: A syndrome characterized by genomic instability, progeroid features, and susceptibility toward early onset hepatocellular carcinoma. {ECO:0000269 PubMed:25261934}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SPRTN

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SPRTN: view

No data available for Genatlas for SPRTN Gene

Publications for SPRTN Gene

  1. Spartan/C1orf124, a reader of PCNA ubiquitylation and a regulator of UV-induced DNA damage response. (PMID: 22681887) Centore RC … Zou L (Molecular cell 2012) 2 3 4 56
  2. DNA-protein crosslink repair: proteases as DNA repair enzymes. (PMID: 25496645) Stingele J … Jentsch S (Trends in biochemical sciences 2015) 2 3 56
  3. Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features. (PMID: 25261934) Lessel D … Kubisch C (Nature genetics 2014) 3 4 56
  4. DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks. (PMID: 23042605) Mosbech A … Mailand N (Nature structural & molecular biology 2012) 3 4 56
  5. Proliferating cell nuclear antigen (PCNA)-binding protein C1orf124 is a regulator of translesion synthesis. (PMID: 22902628) Ghosal G … Chen J (The Journal of biological chemistry 2012) 3 4 56

ExternalLinks

View latest publications for SPRTN gene in Mastermind

Products for SPRTN Gene

  • Addgene plasmids for SPRTN

Sources for SPRTN Gene